My Canon G15, for example, adds the month to the folder number: 123_09, 124_10 and so on.
In fact, your digital camera may already do this for you. But the best option for most people is to store them by the date on which they were taken. If you specialise in photographing a limited range of topics, you might want to organise them by subject.
The final decision depends partly on what sort of photo collection you have. Getting them all under one roof – or into one file directory – is relatively simple, once you have decided how to organise that directory.